Question

How Was This Genomic Region Mapping Image Plotted?

2

Entering edit mode

12.9 years ago

Boboppie ▴ 550

It is originally from this paper. It looks to me was created by photoshop or some advanced image editor. Ideas?

Are there other toolkits or libs available to create nice synteny map or region mapping image like this?

alt text

visualization genome • 2.9k views

ADD COMMENT • link updated 9.6 years ago by Biostar 20 • written 12.9 years ago by Boboppie ▴ 550

score 5 · Answer 1 · 2011-06-21

5

Entering edit mode

12.9 years ago

Pierre Lindenbaum 161k

If you open this image with gimp, and look at "Image properties", you'll see than it has been generated with:

Handmade Software, Inc. Image Alchemy v1.13

so, it comes originally from a PS/PDF/SVG file = from a vectorial drawing editor.( e.g. http:www.inkscape.org) or it as been generated with a dedicated software. (e.g.: http://www.ncrna.org/idiographica/ )

ADD COMMENT • link 12.9 years ago by Pierre Lindenbaum 161k

1

Entering edit mode

Excellent detective work

ADD REPLY • link 12.9 years ago by Casey Bergman 18k

0

Entering edit mode

@pierre cool, thanx!

ADD REPLY • link 12.9 years ago by Boboppie ▴ 550

0

Entering edit mode

metadata... nice idea! ;)

ADD REPLY • link 12.8 years ago by Cjt ▴ 370

score 2 · Answer 2 · 2011-06-21

I am pretty sure it is not automatically generated but "handmade" as there are some minor flaws. Just compare the alignment of the labels to the marker lines on the left. For me it looks like a vector based graphics as done by Adobe Illustrator or the free pendant Inkscape.

For automated drawing you might have a look at osfinder. Maybe this is what you're looking for?

score 1 · Answer 3 · 2011-06-21

1

Entering edit mode

12.9 years ago

Benm ▴ 710

I agree cjt's opinion, it should be "handmade" by SVG or GD module.

I recommend you can use Circos, it is one of the best toolkits to create synteny map for comparative analysis.

ADD COMMENT • link 12.9 years ago by Benm ▴ 710